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Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC‐clone‐based array
Author(s) -
de Ståhl Teresita Díaz,
Sandgren Johanna,
Piotrowski Arkadiusz,
Nord Helena,
Andersson Robin,
Menzel Uwe,
Bogdan Adam,
Thuresson AnnCharlotte,
Poplawski Andrzej,
von Tell Desiree,
Hansson Caisa M.,
Elshafie Amir I.,
ElGhazali Gehad,
Imreh Stephan,
Nordenskjöld Magnus,
Upadhyaya Meena,
Komorowski Jan,
Bruder Carl E.G.,
Dumanski Jan P.
Publication year - 2008
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.20659
Subject(s) - biology , copy number variation , genetics , human genome , genome , comparative genomic hybridization , structural variation , chromosome , 1000 genomes project , segmental duplication , computational biology , gene , genotype , single nucleotide polymorphism , gene family
To further explore the extent of structural large‐scale variation in the human genome, we assessed copy number variations (CNVs) in a series of 71 healthy subjects from three ethnic groups. CNVs were analyzed using comparative genomic hybridization (CGH) to a BAC array covering the human genome, using DNA extracted from peripheral blood, thus avoiding any culture‐induced rearrangements. By applying a newly developed computational algorithm based on Hidden Markov modeling, we identified 1,078 autosomal CNVs, including at least two neighboring/overlapping BACs, which represent 315 distinct regions. The average size of the sequence polymorphisms was ∼350 kb and involved in total ∼117 Mb or ∼3.5% of the genome. Gains were about four times more common than deletions, and segmental duplications (SDs) were overrepresented, especially in larger deletion variants. This strengthens the notion that SDs often define hotspots of chromosomal rearrangements. Over 60% of the identified autosomal rearrangements match previously reported CNVs, recognized with various platforms. However, results from chromosome X do not agree well with the previously annotated CNVs. Furthermore, data from single BACs deviating in copy number suggest that our above estimate of total variation is conservative. This report contributes to the establishment of the common baseline for CNV, which is an important resource in human genetics. Hum Mutat 29(3), 398–408, 2008. © 2007 Wiley‐Liss, Inc.